Research Abstracts Online
January 2010 - March 2011

PI: David D. Thomas, Fellow

Molecular Dynamics of Muscle Proteins

The goal of this research is to understand the structural dynamics associated with force-generating proteins during muscle contraction and to elucidate the molecular mechanisms of catalysis and regulation of the Ca-ATPase (SERCA) that pumps calcium into the sarcoplasmic reticulum and thus relaxes the muscle. Structural and functional models, derived from structural information from x-ray crystallography and electron microscopy, are tested experimentally by an approach based on site-directed labeling and EPR and fluorescence spectroscopy. Specifically, structural models of conformational transitions in muscle proteins are tested and refined by results from the spectroscopic techniques with the aim to detect biologically relevant protein motions. No single method can provide needed information about changes in structure and interactions that occur under functional conditions. A multidisciplinary approach is needed that includes computational simulations that are necessary to connect models with experiment. This work is clearly dependent upon choosing appropriate labeling sites and accurately interpreting spectroscopic data. Molecular dynamics (MD) simulations of spin-labeled proteins have enabled these researchers to accurately predict the shape of electron paramagnetic resonance (EPR) spectra, which means they can design more effective labeling sites for measuring distances and dynamics. Direct simulation of EPR spectra has expanded the ability to interpret ambiguous data. MD simulations have also allowed modeling of structural transitions that occur in response to events such as phosphorylation of muscle regulatory regions or in protein binding. From these MD simulations thermodynamical properties have been determined. The interpretation of spectroscopic data in these systems requires significant computational resources. This project includes ab initio quantum chemistry calculations and molecular dynamics simulations of spectroscopic probes and simulations on large protein complexes.